MolNFT v1 · #143936 · protein
Crystal structure of vacv D13 in complex with rifabutin
6BEC · Scaffold protein D13: “Crystal structure of vacv D13 in complex with rifabutin”. X-ray diffraction, 1 ligand (RBT), 20 pockets (best druggability 0.84). MolNFT v1 #143936 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6BEC
- Type
- protein
- Length
- 1,622 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scaffold protein D13
- UniProt
- P68440
- Ligands
- RBT
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Scaffold protein D13 | protein | 540 | 15% helix, 40% strand | P68440 |
| B | Scaffold protein D13 | protein | 541 | 16% helix, 39% strand | P68440 |
| C | Scaffold protein D13 | protein | 541 | 15% helix, 40% strand | P68440 |
Ligands and binding sites
- RBT · Rifabutin · ligand · chains A, B, C
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C
- FMT · Formic acid · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.84 | 0.85 | 108 | empty |
| 2 | 1094 | 0.84 | 0.85 | 116 | FMT |
| 3 | 1005 | 0.84 | 0.85 | 100 | FMT |
| 4 | 558 | 0.65 | 0.77 | 68 | empty |
| 5 | 138 | 0.49 | 0.79 | 29 | empty |
Interfaces
3 interfaces between chains.
- B–C · 3023 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2853 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 2832 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 6BEC · Crystal structure of VACV D13 in complex with Rifabutin · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P68440
- Elsewhere: RCSB PDB 6BEC · PDBe 6BEC · UniProt P68440
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